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- PDB-6rao: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6... -

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Basic information

Entry
Database: PDB / ID: 6rao
TitleCryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Components
  • Afp1
  • Afp11
  • Afp12
  • Afp2
  • Afp3
  • Afp4
  • Afp5
  • Afp7
  • Afp9
KeywordsVIRUS LIKE PARTICLE / Anti-feeding prophage / secretion system / AFP / contractile
Function / homology
Function and homology information


structural molecule activity
Phage tail sheath C-terminal domain / IraD/Gp25-like / Bacteriophage T4, Gp19, tail tube / Conserved hypothetical protein CHP02241 / Tail sheath protein, C-terminal domain / Tail sheath protein, subtilisin-like domain / Gp25-like family / Gene 25-like lysozyme / Phage tail sheath protein subtilisin-like domain / T4-like virus tail tube protein gp19
Afp12 / Afp11 / Afp9 / Afp7 / Afp5 / Afp4 / Afp3 / Afp2 / Afp1
Biological speciesSerratia entomophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDesfosses, A.
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of an entire contractile injection system in both the extended and contracted states.
Authors: Ambroise Desfosses / Hariprasad Venugopal / Tapan Joshi / Jan Felix / Matthew Jessop / Hyengseop Jeong / Jaekyung Hyun / J Bernard Heymann / Mark R H Hurst / Irina Gutsche / Alok K Mitra /
Abstract: Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, ...Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information on the contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localization variants and perform specific structural comparisons with related systems. We analyse inter-subunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author / em_image_scans
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Afp1
B: Afp1
C: Afp2
D: Afp3
F: Afp5
H: Afp9
E: Afp4
G: Afp7
I: Afp11
J: Afp12


Theoretical massNumber of molelcules
Total (without water)398,23910
Polymers398,23910
Non-polymers00
Water0
1
A: Afp1
B: Afp1
C: Afp2
D: Afp3
F: Afp5
H: Afp9
E: Afp4
G: Afp7
I: Afp11
J: Afp12
x 6


Theoretical massNumber of molelcules
Total (without water)2,389,43760
Polymers2,389,43760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation5
MethodPISA

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Components

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Protein/peptide , 9 types, 10 molecules ABCDFHEGIJ

#1: Protein/peptide Afp1


Mass: 16449.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD8
#2: Protein/peptide Afp2


Mass: 38784.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD7
#3: Protein/peptide Afp3


Mass: 48777.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD6
#4: Protein/peptide Afp5


Mass: 17026.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD4
#5: Protein/peptide Afp9


Mass: 15693.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD0
#6: Protein/peptide Afp4


Mass: 45565.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD5
#7: Protein/peptide Afp7


Mass: 25259.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD2
#8: Protein/peptide Afp11


Mass: 67327.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAC8
#9: Protein/peptide Afp12


Mass: 106905.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAC7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Type: COMPLEX
Details: Note that the needle is not resolved here because of 6-fold symmetry imposition
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Serratia entomophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46991 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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